Table 2 Comparison between HPC pipelines for de novo transcriptome assembly: usability and technical features
From: HPC-T-Assembly: a pipeline for de novo transcriptome assembly of large multi-specie datasets
Tools | GUI for setting parameters | HPC support | Virtual environments | Handling multiple-species datasets | Scalability HPC |
|---|---|---|---|---|---|
transXpress [46] | Not present | Snakemake | Conda | No | Yes |
RNAflow [47] | Not present | Nextflow | Conda and docker/singularity | No | Yes |
Pincho [19] | Not present | SLURM | Not needed | No | Yes |
HPC-T-Assembly | Present (Windows, MacOS, Android, Unix-like) | SLURM | Not needed | Yes | Yes |